Edit-- I just realised this post was from 2016. LoL
Hi, to address your questions:
1. SSH is available via the Azure Portal. Navigate to your web app, and look out for the SSH in the menu on the left under Development Tools. The SSH client is web based.
2. Regarding PHP CLI and composer etc, perhaps a slight tweak to the way you deploy your application in your build and release approach is in order. Try developing locally with composer dependencies etc, push to a repo like Git and then deploy a web app
configured to pull from Git via Deployment Center (via the same left hand menu in Web App on the Azure portal)
3. Azure Web App isn't really intended as a development platform, but it could be if you used the right tools--even if you are on an Open Source stack.
More info can be found at:
https://docs.microsoft.com/en-us/azure/app-service/deploy-local-git
https://docs.microsoft.com/en-us/azure/app-service/containers/app-service-linux-ssh-support
Additionally, if you're looking at leveraging more out of web apps, and need more then just the vanilla service, you could try deploying custom containers:
https://docs.microsoft.com/en-us/azure/app-service/containers/tutorial-custom-docker-image
There's a ready made container that I wrote some time back that runs on Apache and PHP that could get you started if this is right up your alley.
https://hub.docker.com/r/chubbycat/lampodbc
R